Computational Biology
@ Comenius University in Bratislava

Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar. DeepNano-blitz: a fast base caller for MinION nanopore sequencers. Bioinformatics, 36(14):4191-4192. 2020.

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Download from publisher: https://doi.org/10.1093/bioinformatics/btaa297

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Bibliography entry: BibTeX

See also: early version

Abstract:

MOTIVATION: Oxford Nanopore MinION is a portable DNA sequencer that is marketed
as a device that can be deployed anywhere. Current base callers, however, require
a powerful GPU to analyze data produced by MinION in real time, which hampers
field applications. RESULTS: We have developed a fast base caller DeepNano-blitz 
that can analyze stream from up to two MinION runs in real time using a common
laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow 
trading accuracy for speed and the results can be used for real time run
monitoring (i.e. sample composition, barcode balance, species identification,
etc.) or prefiltering of results for more detailed analysis (i.e. filtering out
human DNA from human-pathogen runs). AVAILABILITY AND IMPLEMENTATION:
DeepNano-blitz has been developed and tested on Linux and Intel processors and is
available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz.
CONTACT: vladimir.boza@fmph.uniba.sk. SUPPLEMENTARY INFORMATION: Supplementary
data are available at Bioinformatics online.